Find the CDSes for the first placement; Compute prot consequence using TranslateNAtoAA for each and attach results to nuc_variation.consequnece.

If seq-id specified, use only the placement with the specified id. If ignore_genomic set to true, then consequences will be evaluated for cDNA or MT placements only. Note: Alternatively, the API could be "create and return consequence protein variation(s)", rather than attach, but that for hierarchical input it would be hard to tell which consequence corresponds to which node.

Remap using provided alignment. Ids of at least one row must match. When remapping between transcript/genomic coordiane systems, this method should be used instead of the mapper-based, as if the location is intronic, the method will use the spliced-alignment to create or resolve offset-placement as appropriate.

If this variation has placements defined, return it; otherwise, recursively try parent all the way to the root; return NULL if nothing found. Precondition: root Variation must have been indexed (links to parents defined as necessary)

Apply offsets to the variation's location (variation must be inst) E.g. the original variation could be a transcript location with offsets specifying intronic location. After original transcript lociation is remapped, the offsets are to be applied to the remapped location to get absolute offset-free genomic location.